Tie between Lan and Megaman.EXE (Hub) / Geo and Omega-Xis. Special shoutout to X and Zero too, Megaman has some great duos (including Duo and Duo.EXE).
A really left-field suggestion, but one I have a major soft spot for:
I love the Ritman/Drummond isometric platformers, and arguably Head over Heels is the best of them - although I suspect many people here will have Monster Max on the Game Boy as the one of theirs they're most familiar with.